}
else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
{
- afile = new JSONFile();
+ afile = new JSONFile();
+ // Add groups to AlignFile
+ afile.seqGroups = alignment.getGroups();
+
+ // Add non auto calculated annotation to AlignFile
+ for (AlignmentAnnotation annot : alignment.getAlignmentAnnotation())
+ {
+ if (annot != null && !annot.autoCalculated)
+ {
+ if (annot.label.equals("PDB.CATempFactor"))
+ {
+ continue;
+ }
+ afile.annotations.add(annot);
+ }
+ }
}
else if (format.equalsIgnoreCase("RNAML"))
{
afile.addJVSuffix(jvsuffix);
afile.setSeqs(alignment.getSequencesArray());
- afile.addSeqGroups(alignment);
-
- // Add non auto calculated annotation to AlignFile
- for (AlignmentAnnotation annot : alignment.getAlignmentAnnotation())
- {
- if (!annot.autoCalculated)
- {
- afile.annotations.add(annot);
- }
- }
String afileresp = afile.print();
if (afile.hasWarningMessage())